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Merge pull request #1446 from tripal/tv4g4-issue1444-obo-importer-val…
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…idation

 BUG: Tripal 4 OBO Importer checks for file when none specified in local file field
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@laceysanderson
laceysanderson committed Mar 29, 2023
2 parents b2ed602 + 58066bf commit 0e3d666
Showing 1 changed file with 108 additions and 48 deletions.
156 changes: 108 additions & 48 deletions tripal_chado/src/Plugin/TripalImporter/OBOImporter.php
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Original file line number Diff line number Diff line change
Expand Up @@ -471,71 +471,131 @@ public function formSubmit($form, &$form_state) {
* {@inheritdoc}
*/
public function formValidate($form, &$form_state) {
$public = \Drupal::database();

$obo_id = $form_state->getValue('obo_id');
$obo_name = trim($form_state->getValue('obo_name'));
$obo_url = trim($form_state->getValue('obo_url'));
$obo_file = trim($form_state->getValue('obo_file'));
$uobo_name = trim($form_state->getValue('uobo_name'));
$uobo_url = trim($form_state->getValue('uobo_url'));
$uobo_file = trim($form_state->getValue('uobo_file'));

// Make sure if the name is changed it doesn't conflict with another OBO.
if ($form_state->getTriggeringElement()['#name'] == 'update_obo_details' or
$form_state->getTriggeringElement()['#name'] == 'update_load_obo') {

// Get the current record
$vocab = $public->select('tripal_cv_obo', 't')
->fields('t', ['obo_id', 'name', 'path'])
->condition('name', $uobo_name)
->execute()
->fetchObject();
if ($vocab and $vocab->obo_id != $obo_id) {
$obo_name = trim($form_state->getValue('obo_name') ?? '');
$obo_url = trim($form_state->getValue('obo_url') ?? '');
$obo_file = trim($form_state->getValue('obo_file') ?? '');
$uobo_name = trim($form_state->getValue('uobo_name') ?? '');
$uobo_url = trim($form_state->getValue('uobo_url') ?? '');
$uobo_file = trim($form_state->getValue('uobo_file') ?? '');

// Possible triggering element #name values:
// 'op' from the default submit 'Import OBO File'
// 'update_obo' and 'obo_id' from 'Update Ontology Details'
// 'delete_obo' and 'obo_id' two times from 'Delete Ontology'

// Submitted with 'Update Ontology Details' button
if ($form_state->getTriggeringElement()['#name'] == 'update_obo' ) {

// Make sure if the name is changed it doesn't conflict with another OBO.
$vocab_id = $this->getVocabID($uobo_name);
if ($vocab_id and $vocab_id != $obo_id) {
$form_state->setErrorByName('uobo_name', t('The vocabulary name must be different from existing vocabularies'));
}
// Make sure the file exists. First check if it is a relative path
$dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $uobo_file;
if (!file_exists($dfile)) {
if (!file_exists($uobo_file)) {
$form_state->setErrorByName('uobo_file',
t('The specified path, @path, does not exist or cannot be read.'), ['@path' => $dfile]);
}
// If file specified, make sure it exists, either as a relative or absolute path.
if (!$this->formValidateFile($uobo_file)) {
$form_state->setErrorByName('uobo_file',
t('The specified path, @path, does not exist or cannot be read.', ['@path' => $uobo_file]));
}
if (!$uobo_url and !$uobo_file) {
$form_state->setErrorByName('uobo_url', t('Please provide a URL or a path for the vocabulary.'));
$form_state->setErrorByName('uobo_url', t('Please provide either a URL or a path for the vocabulary.'));
}
if ($uobo_url and $uobo_file) {
$form_state->setErrorByName('uobo_url', t('Please provide only a URL or a path for the vocabulary, but not both.'));
}
}
if ($form_state->getTriggeringElement()['#name'] == 'add_new_obo') {
// Get the current record
$vocab = $public->select('tripal_cv_obo', 't')
->fields('t', ['obo_id', 'name', 'path'])
->condition('name', $obo_name)
->execute()
->fetchObject();
if ($vocab) {
$form_state->setErrorByName('obo_name', t('The vocabulary name must be different from existing vocabularies'));
}
// Make sure the file exists. First check if it is a relative path
$dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo_file;
if (!file_exists($dfile)) {
if (!file_exists($obo_file)) {
$form_state->setErrorByName('obo_file',
t('The specified path, @path, does not exist or cannot be read.'), ['@path' => $dfile]);

// Submitted with 'Import OBO File' button. This is used both for
// reloading a saved ontology and for loading a new ontology.
if ($form_state->getTriggeringElement()['#name'] == 'op') {
if ($uobo_name and $obo_name) {
$form_state->setErrorByName('obo_name', t('New and existing ontologies are both selected, please select only one'));
}
// Generate error if supplied new vocabulary name already exists.
if ($obo_name) {
$vocab_id = $this->getVocabID($obo_name);
if ($vocab_id) {
$form_state->setErrorByName('obo_name', t('The vocabulary name must be different from existing vocabularies'));
}
}
if (!$obo_url and !$obo_file) {
$form_state->setErrorByName('obo_url', t('Please provide a URL or a path for the vocabulary.'));
if ($uobo_name) {
// Validate the update existing ontology section
if (!$uobo_url and !$uobo_file) {
$form_state->setErrorByName('uobo_url', t('Please provide either a URL or a path for the vocabulary.'));
}
if ($uobo_url and $uobo_file) {
$form_state->setErrorByName('uobo_url', t('Please provide only a URL or a path for the vocabulary, but not both.'));
}
// If file specified, make sure it exists, either as a relative or absolute path.
if (!$this->formValidateFile($uobo_file)) {
$form_state->setErrorByName('uobo_file',
t('The specified path, @path, does not exist or cannot be read.', ['@path' => $uobo_file]));
}
}
if ($obo_url and $obo_file) {
$form_state->setErrorByName('obo_url', t('Please provide only a URL or a path for the vocabulary, but not both.'));
else {
// Validate the load new ontology section
if (!$obo_url and !$obo_file) {
$form_state->setErrorByName('obo_url', t('Please provide either a URL or a path for the vocabulary.'));
}
if ($obo_url and $obo_file) {
$form_state->setErrorByName('obo_url', t('Please provide only a URL or a path for the vocabulary, but not both.'));
}
// If file specified, make sure it exists, either as a relative or absolute path.
if (!$this->formValidateFile($obo_file)) {
$form_state->setErrorByName('obo_file',
t('The specified path, @path, does not exist or cannot be read.', ['@path' => $obo_file]));
}
}
}
}

/**
* Returns the obo_id in the tripal_cv_obo table
* from the supplied vocabulary name.
*
* @param string $vocab_name
* The name of the vocabulary to query in the
* public.tripal_cv_obo table.
* @return int
* The obo_id value of the vocabulary, or NULL if this
* vocabulary does not exist.
*/
private function getVocabID($vocab_name) {
$obo_id = NULL;
$public = \Drupal::database();
$vocab = $public->select('tripal_cv_obo', 't')
->fields('t', ['obo_id', 'name', 'path'])
->condition('name', $vocab_name)
->execute()
->fetchObject();
if ($vocab) {
$obo_id = $vocab->obo_id;
}
return $obo_id;
}

/**
* Validates that the passed file specifier exists either as
* specified, or when the default base path is prepended.
* Valid also if no file is specified.
*
* @param string $file
* A file on the local filesystem.
* @return bool
* Returns TRUE if $file exists or if $file evaluates to FALSE.
* Returns FALSE if file identifier does not exist.
*/
private function formValidateFile($file) {
if ($file) {
$checkpath = $_SERVER['DOCUMENT_ROOT'] . base_path() . $file;
if (!file_exists($checkpath) and !file_exists($file)) {
return FALSE;
}
}
return TRUE;
}

/**
* Retrieve a Chado cvterm record using cvterm ID.
*
Expand Down Expand Up @@ -2864,4 +2924,4 @@ private function oboEbiLookup($accession, $type_of_search, $found_iri = NULL, $f
}
return $response;
}
}
}

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